Tbio SDC1 Syndecan-1

Protein Summary

Description

Cell surface proteoglycan that bears both heparan sulfate and chondroitin sulfate and that links the cytoskeleton to the interstitial matrix. Regulates exosome biogenesis in concert with SDCBP and PDCD6IP (PubMed:22660413). The protein encoded by this gene is a transmembrane (type I) heparan sulfate proteoglycan and is a member of the syndecan proteoglycan family. The syndecans mediate cell binding, cell signaling, and cytoskeletal organization and syndecan receptors are required for internalization of the HIV-1 tat protein. The syndecan-1 protein functions as an integral membrane protein and participates in cell proliferation, cell migration and cell-matrix interactions via its receptor for extracellular matrix proteins. Altered syndecan-1 expression has been detected in several different tumor types. While several transcript variants may exist for this gene, the full-length natures of only two have been described to date. These two represent the major variants of this gene and encode the same protein. [provided by RefSeq, Jul 2008]

Uniprot Accession IDs

• P18827
• D6W523
• Q53QV0
• Q546D3
• Q96HB7
• SYND1

Gene Name

• SDC1

Ensembl ID

• ENST00000254351
• ENSP00000254351
• ENSG00000115884
• ENST00000381150
• ENSP00000370542

Symbol

• SDC
• SDC
• CD138
• SYND1
• syndecan

Knowledge Table

Most Knowledge About	Knowledge Value (0 to 1 scale)
transcription factor perturbation	0.94
kinase perturbation	0.93
biological process	0.91
disease perturbation	0.87
transcription factor binding site profile	0.82

Protein Classes

PANTHER Classes

Protein / Signaling Molecule / Membrane-bound Signaling Molecule / Syndecan-1

Protein / Extracellular Matrix Protein / Extracellular Matrix Glycoprotein / Syndecan-1

Protein / Defense/immunity Protein / Syndecan-1

Protein / Cytoskeletal Protein / Syndecan-1

Protein / Cell Adhesion Molecule / Syndecan-1

DTO Classes

Protein / Extracellular Structure / Extracellular Matrix Glycoprotein / Syndecan-1

IDG Development Level Summary

Tdark

These are targets about which virtually nothing is known. They do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 2915.76   (req: < 5)

Gene RIFs: 258   (req: <= 3)

Antibodies: 1362   (req: <= 50)

Tbio

These targets do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 2915.76   (req: >= 5)

Gene RIFs: 258   (req: > 3)

Antibodies: 1362   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 21

Tchem

Target has at least one ChEMBL compound with an activity cutoff of < 30 nM - AND - satisfies the preceding conditions

Active Ligand: 0

Tclin

Target has at least one approved drug - AND - satisfies the preceding conditions

Active Drug: 0

Expression Data (0 Tissues)

tutorial

No expression data found

Protein Sequence and Structure

Residue Counts

Protein Sequence

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Related Tools (4)

Target Illumination GWAS Analytics (TIGA)

TIGA scores and ranks GWAS discovered associations according to the quantity and quality of the evidence supporting the association.

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GENEVA

GENEVA (GENe Expression Variance Analysis) allows you to identify RNA-sequencing datasets from the Gene Expression Omnibus (GEO) that contain conditions modulating a gene or a gene signature.

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GlyGen

GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data.

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ARCHS4

ARCHS4 provides access to gene-function predictions based on RNA-seq co-expression, and gene expression levels across cell and tissues.

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Approved Drugs (0)

No approved drugs found

Active Ligands (0)

No active ligands found

Protein-Protein Interactions (320)

Explore Interacting Targets

1 – 10 of 320

• See Interactions on String-DB

HADHA

Tbio

Novelty:  0.00385746

p_int:  0.999999794

p_ni:  6.4e-8

p_wrong:  1.43e-7

Data Source:  BioPlex

FARP1

Tbio

Novelty:  0.04040696

p_int:  0.999995054

p_ni:  0.000004946

Score:  0.257

Data Source:  BioPlex,STRINGDB

DHRS2

Tbio

Family:  Enzyme

Novelty:  0.002032

p_int:  0.999978149

p_ni:  0.000008227

p_wrong:  0.000013624

Score:  0.313

Data Source:  BioPlex,STRINGDB

GMEB2

Tdark

Family:  TF

Novelty:  0.1945427

p_int:  0.999970602

p_ni:  0.000028782

p_wrong:  6.16e-7

Score:  0.663

Data Source:  BioPlex,STRINGDB

FGF2

Tchem

Novelty:  0.00007856

p_int:  0.999918517

p_ni:  0.00000195

p_wrong:  0.000079534

Score:  0.981

Data Source:  BioPlex,STRINGDB

PRDM10

Tbio

Family:  TF; Epigenetic

Novelty:  0.03463517

p_int:  0.99975567

p_ni:  0.000244327

p_wrong:  3e-9

Score:  0.299

Data Source:  BioPlex,STRINGDB

CYHR1

Tdark

Novelty:  0.04771996

p_int:  0.999722829

p_ni:  0.000275122

p_wrong:  0.000002049

Data Source:  BioPlex

EPHA2

Tclin

Family:  Kinase

Novelty:  0.00191002

p_int:  0.998340724

p_ni:  0.001659276

Score:  0.414

Data Source:  BioPlex,STRINGDB

CSNK1G3

Tchem

Family:  Kinase

Novelty:  0.07584067

p_int:  0.997757967

p_ni:  0.002242033

Data Source:  BioPlex

OCLN

Tbio

Novelty:  0.00047671

p_int:  0.997355459

p_ni:  0.002644539

p_wrong:  2e-9

Score:  0.267

Data Source:  BioPlex,STRINGDB

Nearest Tclin Targets (8)

Explore Nearest Tclin Targets

Upstream (7)

Downstream (1)

1 – 5 of 7

MAP2K2

Tclin

Family:  Kinase

KEGG Distance:  3

Common Pathways:  1

1: Proteoglycans in cancer

MAP2K1

Tclin

Family:  Kinase

KEGG Distance:  3

Common Pathways:  1

1: Proteoglycans in cancer

IGF1R

Tclin

Family:  Kinase

KEGG Distance:  3

Common Pathways:  1

1: Proteoglycans in cancer

FGFR1

Tclin

Family:  Kinase

KEGG Distance:  3

Common Pathways:  1

1: Proteoglycans in cancer

RAF1

Tclin

Family:  Kinase

KEGG Distance:  3

Common Pathways:  1

1: Proteoglycans in cancer

Pathways (52)

Reactome (33)

KEGG (5)

PathwayCommons (14)

A tetrasaccharide linker sequence is required for GAG synthesis (R-HSA-1971475)

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Find Similar Targets

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5

1 – 5 of 33

Data Source	Name	Explore in Pharos	Explore in Source
Reactome	A tetrasaccharide linker sequence is required for GAG synthesis	26 targets	R-HSA-1971475
Reactome	Cell surface interactions at the vascular wall	211 targets	R-HSA-202733
Reactome	Chondroitin sulfate/dermatan sulfate metabolism	50 targets	R-HSA-1793185
Reactome	Cytokine Signaling in Immune system	922 targets	R-HSA-1280215
Reactome	Defective B3GALT6 causes EDSP2 and SEMDJL1	20 targets	R-HSA-4420332

Name	Explore in Pharos	Explore in Source
A tetrasaccharide linker sequence is required for GAG synthesis	26 targets	R-HSA-1971475
Cell surface interactions at the vascular wall	211 targets	R-HSA-202733
Chondroitin sulfate/dermatan sulfate metabolism	50 targets	R-HSA-1793185
Cytokine Signaling in Immune system	922 targets	R-HSA-1280215
Defective B3GALT6 causes EDSP2 and SEMDJL1	20 targets	R-HSA-4420332

Viral Interactions (0)

No viral interactions found

Gene Ontology Terms (29)

Functions (2)

Components (8)

Processes (19)

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10

1 – 2 of 2

GO Term	Evidence	Assigned by
identical protein binding	Inferred from Physical Interaction (IPI)	IntAct
protein C-terminus binding	Inferred from Physical Interaction (IPI)	UniProtKB

Disease Associations (null)

No disease associations found

GWAS Traits (37)

• Explore on Target Illumination GWAS Analytics (TIGA)

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5

1 – 5 of 37

GWAS Trait	EFO ID	Study Count	SNP Count	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
high density lipoprotein cholesterol measurement	EFO_0004612	31	6	31		91
sex hormone-binding globulin measurement	EFO_0004696	6	3	6		87.6
low density lipoprotein cholesterol measurement	EFO_0004611	5	4	6		85.4
testosterone measurement	EFO_0004908	6	2	5	7.8	83.3
apolipoprotein A 1 measurement	EFO_0004614	2	3	3		82.2

• Explore on Target Illumination GWAS Analytics (TIGA)

Items per page:

5

1 – 5 of 37

GWAS Trait	EFO ID	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
high density lipoprotein cholesterol measurement	EFO_0004612	31		91
sex hormone-binding globulin measurement	EFO_0004696	6		87.6
low density lipoprotein cholesterol measurement	EFO_0004611	6		85.4
testosterone measurement	EFO_0004908	5	7.8	83.3
apolipoprotein A 1 measurement	EFO_0004614	3		82.2

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UniProt Keyword Find Similar Targets

No Header	No Header
3D-structure
Complete proteome
Glycoprotein
Heparan sulfate
Membrane
Phosphoprotein
Polymorphism
Proteoglycan
Reference proteome
Secreted

GWAS Trait Find Similar Targets

No Header	No Header
apolipoprotein A 1 measurement
apolipoprotein B measurement
appendicular lean mass
balding measurement
BMI-adjusted hip circumference
body mass index
central corneal thickness
cholesterol:total lipids ratio
cholesteryl ester measurement
cholesteryl esters:total lipids ratio

MGI Phenotype Find Similar Targets

No Header	No Header
cellular phenotype
hematopoietic system phenotype
homeostasis/metabolism phenotype
immune system phenotype
mortality/aging
vision/eye phenotype

IDG Resources

No IDG generated resources found

Orthologs (10)

1 – 5 of 10

Species	Name	Source ID	Gene ID	OMA	EggNOG	Inparanoid
Macaque	syndecan 1		701544
Mouse	syndecan 1	MGI:1349162	20969
Rat	syndecan 1	RGD:3648	25216
Dog	syndecan 1	VGNC:45942	482986
Horse	syndecan 1	VGNC:22761	100071892

Species	Name	OMA	EggNOG	Inparanoid
Macaque	syndecan 1
Mouse	syndecan 1
Rat	syndecan 1
Dog	syndecan 1
Horse	syndecan 1

Publication Statistics

PubMed Score 2915.76

PubMed score by year

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PubTator Score 1001.13

PubTator score by year

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Related Publications

Text Mined References (303)

GeneRif Annotations (258)

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PMID	Year	Title